• How we have used R Markdown in our undergraduate courses

• Reproducibility with R Markdown

• And some things that we think are just cool in Rmd.

• BIG Thank you to Project TIER and the Alfred P. Sloan Foundation

• One-stop solution

• Work is reproducible

• Calibrated for collaboration

• Free (p = 0)

• Broad and used in industry (unlike Stata)

• Learning Curve?
• Packages facilitate learning:
• tidyverse, mosaic, stargazer
• error detection
• autocomplete
• online educational courses

• Stata and dyndoc (Stata 15)?
• not a reasonable alternative

• Python and Jupyter Notebooks
• also free
• not geared to statistical programming
• good for theory & visualization
• plays well with R & R Studio (reticulated Python)

Michael O'Hara:

Senior thesis seminar with 9 students

• Very little background
• All stages in R Markdown
  • Data manipulation, visualization, analysis
  • Presentations
  • Final paper

Advantages:

• To students
  • One environment for everything
• To me
  • Full reproducibility of all 9 papers (one award)
  • Much easier to reproduce in one document
  • Very professional appearance (with template)

Cost

• Somewhat higher startup cost in teaching them R and R Studio

• Create slides in an Econometrics course
• Final project in senior research seminar
• Create custom progress reports for students
• Interactive shiny apps for micro students

• A course in Behavioral Economics
• Slides, notes and assignments
• Students do a reproducible research project
• They reproduce the results of a published paper and propose a new experimental design to test a new hypothesis

• A course in Behavioral Economics
• Slides, notes and assignments
• Students do a reproducible research project
• They reproduce the results of a published paper and propose a new experimental design to test a new hypothesis

• What happens in a traditional research report?
• Are traditional research reports easily reproducible?
• What gives us soup to nuts reproducibility?
• Answer: R Markdown or Scripted LaTeX + STATA (StatTag?)
• Works within the TIER framework
• I've implemented a variation of this in an upper-level economics elective

# Header 1

## Header 2

### Header 3

This is normal sized text used in the body of our work. 

For bullet points, we use dashes, e.g. 

- Intro to RStudio
- More content
  - a sub-point
- Back to the original level

R Markdown can produce a variety of document types (other than the default html page):

• pdf_document makes a PDF with LaTeX (.pdf)

• word_document for Microsoft Word documents (.docx).

• odt_document for OpenDocument Text documents (.odt).

• rtf_document for Rich Text Format documents (.rtf)

And others.

R Markdown can also be re-purposed to produce a presentation file (as with this presentation):

• io_slides opens in your browser and interactive (.html)

• slidy another browser based presentation format (.html)

• beamer makes a PDF with LaTeX (.pdf)

Think about data analysis as falling into three loose categories:

• management & wrangling
• visualization & summary statistics
• modeling & inference

All of this occurs in the code "chunk"

• To open a code chunk hit CMD + OPTION + I on a Mac

• Or type out three backticks ``` folowed by {r}

• And then three more back ticks ``` on another line.

• Within the {r} you can specify options, like {eval = FALSE} if you don't want it to evaluate the code

• Or you can label the code chunk, e.g. {r cars} labels the chunk "cars" in your ToC

```{r cars, echo = TRUE}
summary(cars)
```

The option echo = TRUE means that the code gets included in the rendered html.

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

##   session subject  r1  r2  r3  r4  r5  r6  r7  r8  r9  treatment team
## 1       1       1   0   0   0   0  10  10   0   0   0 individual   NA
## 2       1       2   0   0  30  40  40   0   0   0  20 individual   NA
## 3       1       3  30  30   0   0   0  60  60  10   0 individual   NA
## 4       1       4  20   0 100   0   0  30  75 100 100 individual   NA
## 5       1       5 100 100 100 100 100 100 100 100 100 individual   NA
## 6       1       6 100 100 100 100 100 100 100   0   0 individual   NA
##           uniqid
## 1 1_individual_1
## 2 1_individual_2
## 3 1_individual_3
## 4 1_individual_4
## 5 1_individual_5
## 6 1_individual_6

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  value by treatment
## W = 52876, p-value = 3.838e-10
## alternative hypothesis: true location shift is not equal to 0

## 
## Call:
## lm(formula = value ~ treatment, data = SutNarrow)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -61.370 -29.385  -0.542  38.630  60.615 
## 
## Coefficients:
##                    Estimate Std. Error t value Pr(>|t|)    
## (Intercept)          39.385      1.451  27.152  < 2e-16 ***
## treatmentmessage     21.985      1.994  11.028  < 2e-16 ***
## treatmentmixed       10.609      1.925   5.510 3.92e-08 ***
## treatmentpaycomm     10.886      2.144   5.077 4.09e-07 ***
## treatmentteamtreat   16.313      2.629   6.204 6.34e-10 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 34.81 on 2713 degrees of freedom
## Multiple R-squared:  0.04473,    Adjusted R-squared:  0.04333 
## F-statistic: 31.76 on 4 and 2713 DF,  p-value: < 2.2e-16

## Oneway (time) effect Random Effect Model 
##    (Swamy-Arora's transformation)
## 
## Call:
## plm(formula = value ~ treatment, data = SutNarrow, effect = "time", 
##     model = "random", index = c("uniqid"))
## 
## Balanced Panel: n = 302, T = 9, N = 2718
## 
## Effects:
##                    var  std.dev share
## idiosyncratic 1197.631   34.607 0.987
## time            16.062    4.008 0.013
## theta: 0.555
## 
## Residuals:
##     Min.  1st Qu.   Median  3rd Qu.     Max. 
## -61.9325 -28.6639  -2.5889  33.7276  64.3014 
## 
## Coefficients:
##                    Estimate Std. Error t-value  Pr(>|t|)    
## (Intercept)         39.3854     1.9657 20.0367 < 2.2e-16 ***
## treatmentmessage    21.9850     1.9818 11.0936 < 2.2e-16 ***
## treatmentmixed      10.6093     1.9140  5.5430 3.259e-08 ***
## treatmentpaycomm    10.8862     2.1315  5.1072 3.497e-07 ***
## treatmentteamtreat  16.3130     2.6138  6.2412 5.022e-10 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Total Sum of Squares:    3403100
## Residual Sum of Squares: 3249200
## R-Squared:      0.045244
## Adj. R-Squared: 0.043836
## F-statistic: 32.1409 on 4 and 2713 DF, p-value: < 2.22e-16

How about Bayes' Rule?

\[Pr(\mbox{Outcome} | \mbox{signal}) = \frac{\theta p}{\theta p - (1 - \theta)(1 - p)}\]

R Markdown uses \(\LaTeX\) for math and it immediately gets displayed in R Studio.

That is, \(\LaTeX\) without the challenges of learning the packages, tables, etc that makes learning \(\LaTeX\) so hard.

In-line equations are bracketed by single dollar signs $.

Off-set equations are bracketed by double dollar signs $$.

R Markdown and R Studio together have excellent capabilities.

• R Studio can show you the output of the commands within the R Markdown file
• R Studio has error-detection and debugging assistance for your code (unlike, e.g. STATA or aspects of Excel)
• R Studio server can be hosted online and your students work with logins there

Michael:

• Students will only learn commands through graded assignments

Aaron:

• Students can struggle with basic computing (working directory, etc.); but autocomplete helps

Students have to adjust to get Basics Right

• File paths - many students haven’t had to specify a file path before (``drag-and-dropitis'') (initial inequality in baselines can be tough)
• Difference between a script (.R file - like a .do file) and a markdown document/notebook (.Rmd) (medium adjustment)
• Difference between the .Rmd and the exported file: pdf, html, etc (quick adjustment)

Students like (or are used to) WYSIWYG, which Rmd is not - Students are accustomed to MS Word & G docs which are WYSIWYG, but Rmd is not.

Installing packages

• analogy: you have to install apps (packages) to do different things on your (RStudio & R)
• Chrome extensions

Server = REALLY GREAT!

New to R?

• Check out the Computation and Visualization Consortium's week-long workshop over the summer (dates June 12-16, Macalaster College - Kaplan, Prium & Horton)
• Consider subscribing to classes at Datacamp.com (take the intro free of charge)
• Grolemund & Wickham, 2016, R for Data Science, r4ds
• Baumer, Horton & Kaplan, forthcoming, Modern Data Science with R.

We took inspiration from many people along the way. We thank them and ask their forgiveness.

• Andrew Bray – Reproducibility 2.0
• Nick Horton – Getting Started with R and R Md
• Mine Çetinkaya-Rundel – website
• Hadley Wickham & Garrett Grolemund – r4ds
• Danny Kaplan – DataComputing
• Amelia McNamara – website
• Ben Baumer – website
• Cosma Shalizi – R Markdown for Class Reports
• Randy Prium – website